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Marie Chevereau-Choquet,1 Benjamin Thoreau,2,3 Camille Taillé,4,5 Sylvain Marchand-Adam,1,6 Hugues Morel,7 Laurent Plantier,1,6,* Laurent Portel8,* 1Service de Pneumologie et Explorations Fonctionnelles Respiratoires, CHRU de Tours, Tours, France; 2Service de Médecine Interne, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP, Hôpital Cochin, Paris, France; 3Inserm U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France; 4Service de Pneumologie A, AP-HP Nord, Hôpital Bichat Claude Bernard, Paris, France; 5Inserm U1152, Université Paris Cité, Paris, France; 6CEPR, Inserm UMR1100, Université de Tours, Tours, France; 7Service de Pneumologie, CHR d’Orléans, Orléans, France; 8Service de Pneumologie, Centre Hospitalier Robert Boulin, Libourne, France*These authors contributed equally to this workCorrespondence: Laurent Plantier, Service de Pneumologie et Explorations Fonctionnelles Respiratoires, CHRU de Tours, 2 Bd Tonnellé, Tours, 37044, France, Email laurent.plantier@univ-tours.frPurpose: Severe asthma affects 5 to 10% of asthmatics and accounts for a large part of asthma-related morbidity and costs. The determinants of asthma severity are poorly understood. We tested the hypothesis that asthma severity was associated with 1) atopy and allergy and 2) markers associated with environmental exposure.Patients and Methods: Data from the FASE-CPHG study, a cross-sectional, observational, multicenter investigation, were analyzed to identify markers associated with asthma severity. Asthma severity was gauged using the ASSESS score, encompassing symptom control, exacerbations, FEV1 and therapeutic load. Bivariate and multivariate analyses were used to identify patient characteristics associated with the ASSESS score.Results: The analysis involved 948 patients, with 592 women, of which 447 patients (47%) had severe asthma. Among these, 491 patients (52%) had at least one positive aeroallergen skin prick test and 525 (55%) had at least one allergic disease among atopic dermatitis, chronic rhinitis and food allergy. The mean±SD ASSESS score was 11.2± 3.4. Characteristics associated with a higher ASSESS score were female sex, secondary or lower education, unemployed occupational status, smoking, work-aggravated asthma and urban housing. There was no association between the ASSESS score and allergic diseases, aeroallergen-specific skin prick tests and IgEs, or blood eosinophil counts.Conclusion: While atopy and allergy were frequent among asthmatics, neither was associated with asthma severity. Modifiable environmental factors such as smoking, urban housing and work-aggravated asthma were independently associated with asthma severity.Keywords: allergy, ASSESS, asthma, environment, severity

Although carbapenemase-producing Enterobacteriaceae (CPE) have become a serious public health issue, their detection remains challenging. The aim of this study was to implement a test based on imipenem hydrolysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS), using 65 strains producing or not a carbapenemase. Then, we compared its performance to that of the Rapidec Carba NP test using 20 additional strains. The MS-based test effectively discriminated between CPE and other non-carbapenem-susceptible strains compared to the Rapidec Carba NP test (sensitivity 100% and 92%, specificity 94% and 92%, respectively). The MS-based test gave less difficulty in interpretation than the colorimetric Rapidec Carba NP test. MALDI-ToF gave a result in less than one hour and limited the use of expensive molecular assays. In conclusion, the hydrolysis test based on MALDI-ToF MS can detect clinically relevant CPE isolates in routine practice. This technology, also described to screen for carbapenem resistance in Pseudomonas aeruginosa and Acinetobacter baumannii complex strains, also seems to be interesting in routine practice for these pathogens. [ABSTRACT FROM AUTHOR]

Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target-capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP-based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re-assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Two Calanus species, C. glacialis and C. finmarchicus, due to different life strategies and environmental preferences act as an ecological indicators of Arctic Atlantification. Their high lipid content makes them important food source for higher trophic levels of Arctic ecosystems including the most abundant Northern Hemisphere's seabird, the little auk (Alle alle). Recent studies indicate a critical need for the use of molecular methods to reliably identify these two sympatric Calanus species. We performed genetic and morphology-based identification of 2600 Calanus individuals collected in little auks foraging grounds and diet in summer seasons 2019-2021 in regions of Svalbard with varying levels of Atlantification. Genetic identification proved that 40% of Calanus individuals were wrongly classified as C. finmarchicus according to morphology-based identification in both types of samples. The diet of little auks consisted almost entirely of C. glacialis even in more Atlantified regions. Due to the substantial bias in morphology-based identification, we expect that the scale of the northern expansion of boreal C. finmarchicus may have been largely overestimated and that higher costs for birds exposed to Atlantification could be mostly driven by a decrease in the size of C. glacialis rather than by shift from C. glacialis to C. finmarchicus., (© 2023. Springer Nature Limited.)

We used ancient DNA (aDNA) extraction methods to sequence museum voucher samples of Oligobrachia webbi, a frenulate siboglinid polychaete described from a northern Norwegian fjord over fifty years ago. Our sequencing results indicate a genetic match with the cryptic seep species, Oligobrachia haakonmosbiensis (99% pairwise identity for 574 bp mtCOI fragments) . Due to its similarity with O. webbi , the identity of O. haakonmosbiensis has been a matter of debate since its description, which we have now resolved. Furthermore, our results demonstrate that chemosynthesis-based siboglinids, that constitute the bulk of the biomass at Arctic seeps are not seep specialists. Our data on sediment geochemistry and carbon and nitrogen content reveal reduced conditions in fjords/sounds, similar to those at seep systems. Accumulation and decomposition of both terrestrial and marine organic matter results in the buildup of methane and sulfide that apparently can sustain chemosymbiotic fauna. The occurrence of fjords and by extension, highly reducing habitats, could have led to Arctic chemosymbiotic species being relatively generalist with their habitat, as opposed to being seep or vent specialists. Our stable isotope analyses indicate the incorporation of photosynthetically derived carbon in some individuals, which aligns with experiments conducted on frenulates before the discovery of chemosynthesis that demonstrated their ability to take up organic molecules from the surrounding sediment. Since reduced gases in non-seep environments are ultimately sourced from photosynthetic processes, we suggest that the extreme seasonality of the Arctic has resulted in Arctic chemosymbiotic animals seasonally changing their degree of reliance on chemosynthetic partners. Overall, the role of chemosynthesis in Arctic benthos and marine ecosystems and links to photosynthesis may be complex, and more extensive than currently known., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors.)

Introduction: Pulmonary alveolar proteinosis (PAP) is a rare disease characterized by alveolar accumulation of lipoproteinaceous material, caused by a macrophagic clearance disorder. We present a case of PAP in a patient taking the immunosuppressant drug mycophenolate mofetil (MMF) in the context of invasive pulmonary aspergillosis, of which we discuss the pathophysiology and treatment as reported in the literature., Case Report: A 43-year-old man with cardiomyopathy received a heart transplant and was treated by MMF, tacrolimus and corticosteroids. Three months after the transplant, he presented with acute oxygen-dependent respiratory failure. The diagnosis of PAP seemed likely on the CT scan and was confirmed by bronchoalveolar lavage, as was the diagnostic of invasive pulmonary aspergillosis (IPA). However, GM-CSF autoantibodies were not found. As there existed a suspicion of MMF imputability, the treatment was discontinued and an antifungal treatment was started. The patient was reassessed one month after discontinuation of MMF and found to have clinically and radiologically improved. Four other cases of MMF-induced PAP have been reported in the literature., Conclusions: MMF and IPA could be predisposing cofactors for the occurrence of secondary PAP., (Copyright © 2022 SPLF. Published by Elsevier Masson SAS. All rights reserved.)

Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbps). As an alternative to whole-genome sequencing in Calanus spp., we sequenced and de novo assembled transcriptomes of five Calanus species: Calanus glacialis , C. hyperboreus , C. marshallae , C. pacificus , and C .  helgolandicus . Functional assignment of protein families based on clusters of orthologous genes (COG) and gene ontology (GO) annotations showed analogous patterns of protein functions across species. Phylogenetic analyses using maximum likelihood (ML) of 191 protein-coding genes mined from RNA-seq data fully resolved evolutionary relationships among seven Calanus species investigated (five species sequenced for this study and two species with published datasets), with gene and site concordance factors showing that 109 out of 191 protein-coding genes support a separation between three groups: the C .  finmarchicus group (including C .  finmarchicus , C. glacialis , and C. marshallae ), the C .  helgolandicus group (including C .  helgolandicus , C. sinicus , and C .  pacificus ) and the monophyletic C. hyperboreus group. The tree topology obtained in ML analyses was similar to a previously proposed phylogeny based on morphological criteria and cleared certain ambiguities from past studies on evolutionary relationships among Calanus species., Competing Interests: The authors declare they have no conflict of interest., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Overexpression of efflux pumps extruding antibiotics currently used for the treatment of Acinetobacter baumannii infections has been described as an important mechanism causing antibiotic resistance. The first aim of this work was to phenotypically evaluate the overexpression of efflux pumps on a collection of 124 ciprofloxacin-resistant A. baumannii strains. An overexpression of genes encoding one or more efflux pumps was obtained for 19 out of the 34 strains with a positive phenotypic efflux (56%). The most frequent genes overexpressed were those belonging to the RND family, with adeJ being the most prevalent (50%). Interestingly, efflux pump genes coding for MATE and MFS families were also overexpressed quite frequently: abeM (32%) and abaQ (26%). The second aim was to synthesize 1-(1-naphthylmethyl)-piperazine analogs as potential new efflux pump inhibitors and biologically evaluate them against strains with a positive phenotypic efflux. Quinoline and pyridine analogs were found to be more effective than their parent compound, 1-(1-naphthyl methyl)-piperazine. Stereochemistry also played an important part in the inhibitory activity, as quinoline derivative ( R )-3a was identified as being the most effective and less cytotoxic. Its inhibitory activity was also correlated with the number of efflux pumps expressed by a strain. The results obtained in this work suggest that quinoline analogs of 1-(1-naphthylmethyl)-piperazine are promising leads in the development of new anti-Acinetobacter baumannii therapeutic alternatives in combination with antibiotics for which an efflux-mediated resistance is suspected.

Purpose of the Report: We aimed to evaluate the role of 18F-FDG PET/CT in predicting patient outcome following chimeric antigen receptor T (CAR T) cells infusion in aggressive B-cell lymphoma., Methods: 18F-FDG PET/CT data before leukapheresis, before CAR T-cell infusion and 1 month (M1) after CAR T-cell infusion, from 72 patients were retrospectively analyzed. SUVmax, total lesion glycolysis (TLG), metabolic tumor volume (MTV), and parameters describing tumor kinetics were calculated for each 18F-FDG PET/CT performed. The aim was to evaluate the prognostic value of 18F-FDG PET/CT metabolic parameters for predicting progression-free survival (PFS) and overall survival (OS) following CAR T-cell therapy., Results: Regarding PFS, ∆MTVpre-CAR and ∆TLGpre-CAR were found to be more discriminating compared with metabolic parameters at preinfusion. Median PFS in patients with a ∆MTVpre-CAR of less than 300% was 6.8 months (95% confidence interval [CI], 2.8 months to not reached) compared with 2.8 months (95% CI, 0.9-3.0 months) for those with a value of 300% or greater (P = 0.004). Likewise, median PFS in patients with ∆TLGpre-CAR of less than 420% was 6.8 months (95% CI, 2.8 months to not reached) compared with 2.7 months (95% CI, 1.3-3.0 months) for those with a value of 420% or greater (P = 0.0148). Regarding OS, metabolic parameters at M1 were strongly associated with subsequent outcome. SUVmax at M1 with a cutoff value of 14 was the most predictive parameter in multivariate analysis, outweighing other clinicobiological variables (P < 0.0001)., Conclusions: Disease metabolic volume kinetics before infusion of CAR T cells seems to be superior to initial tumor bulk itself for predicting PFS. For OS, SUVmax at M1 might adequately segregate patients with different prognosis., Competing Interests: Conflicts of interest and sources of funding: P. Sesques: honoraria, advisory/consultancy from Novartis and Kite/Gilead; F.W.: honoraria, advisory/consultancy from Novartis and Kite/Gilead; V. Schwiertz: honoraria, advisory/consultancy from Kite/Gilead and Novartis; G.S.: advisory board/consulting for Gilead, Kite, Novartis; E.B.: honoraria, consultancy from Gilead, Novartis. The other authors have none declared., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Whole-genome sequencing is still often a difficult, costly and time-consuming task. The emergence of various genome reduced-representation sequencing (RRS) protocols such as restriction site-associated DNA sequencing (RADseq) has facilitated the access to genome-wide information, without the need for whole-genome sequencing. Reaching the full potential of RRS protocols though requires adjustments and tailoring to the species under investigation. To that end, simulation software has been developed to guide researchers in the customization of their RADseq experiment, but the extent to which these tools mimic the behaviour of a protocol in generating sequencing data is limited. In this current issue of Molecular Ecology Resources, Rivera-Colón et al. (2020) introduce RADinitio, a new software for simulating RADseq data designed to perform simulations at the highest level of representativeness. By taking into account the effects of library preparation and sequencing parameters on the resulting sequences, RADinitio allows the precise identification of the sources of failure when designing a RADseq experiment. This new software represents a considerable advance in RADseq data simulation and will likely lead to increased success in RADseq experiments., (© 2020 John Wiley & Sons Ltd.)

Late developmental stages of the marine copepods in the genus Calanus can spend extended periods in a dormant stage (diapause) that is preceded by the accumulation of large lipid stores. We assessed how lipid metabolism during development from the C4 stage to adult is altered in response to predation risk and varying food availability, to ultimately understand more of the metabolic processes during development in Calanus copepods. We used RNA sequencing to assess if perceived predation risk in combination with varied food availability affects expression of genes associated with lipid metabolism and diapause preparation in C. finmarchicus. The lipid metabolism response to predation risk differed depending on food availability, time and life stage. Predation risk caused upregulation of lipid catabolism with high food, and downregulation with low food. Under low food conditions, predation risk disrupted lipid accumulation. The copepods showed no clear signs of diapause preparation, supporting earlier observations of the importance of multiple environmental cues in inducing diapause in C. finmarchicus. This study demonstrates that lipid metabolism is a sensitive endpoint for the interacting environmental effects of predation pressure and food availability. As diapause may be controlled by lipid accumulation, our findings may contribute towards understanding processes that can ultimately influence diapause timing.

Two autologous anti-CD19 chimeric antigen receptors (CAR) T cells (axicabtagene ciloleucel [axi-cel] and tisagenlecleucel [tisa-cel]) are commercially approved in Europe for relapsed/refractory (R/R) diffuse large B cell lymphoma (DLBCL). We performed a retrospective study to evaluate patterns of use, efficacy and safety for axi-cel and tisa-cel. Data from 70 patients who underwent apheresis for commercial CAR T cells between January 2018 and November 2019 in our institution were retrospectively collected. Sixty-one patients were infused. The median age at infusion was 59 years old (range 27-75 years). The median number of prior therapies was 3 (range, 2-6). The overall response rates (ORRs) at 1 month and 3 months were 63% and 45%, respectively, with 48% and 39% achieving a complete response (CR), respectively. After a median follow-up after infusion of 5.7 months, the median progression-free survival (PFS) was 3.0 months (95% CI, 2.8-8.8 months), and the median overall survival (OS) was 11.8 months (95% CI, 6.0-12.6 months). In multivariate analysis, factors associated with poor PFS were the number of previous lines of treatment before CAR T cells (≥4) (P = .010) and a C reactive protein (CRP) value >30 mg/L at the time of lymphodepletion (P < .001). Likewise, the only factor associated with a shorter OS was CRP >30 mg/L (P = .009). Cytokine release syndrome (CRS) of any grade occurred in 85% of patients, including 8% of patients with CRS of grade 3 or higher. Immune cell-associated neurotoxicity syndrome (ICANS) of any grade occurred in 28% of patients, including 10% of patients with ICANS of grade 3 or higher. Regarding efficacy and safety, no significant difference was found between axi-cel and tisa-cel. This analysis describes one of the largest real-life cohorts of patients treated with axi-cel and tisa-cel for R/R aggressive B cell lymphoma in Europe., (© 2020 Wiley Periodicals LLC.)

Background: The SARS-CoV-2 (Severe Acute Respiratory Syndrome CoronaVirus 2) is responsible for the infectious respiratory disease called COVID-19 (COronaVIrus Disease 2019). In response to the growing COVID-19 pandemic, point-of-care (POC) tests have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. We conducted a prospective observational study to evaluate the performance of two POC tests, COVID-PRESTO® and COVID-DUO®, compared to the gold standard, RT-PCR (real-time reverse transcriptase polymerase chain reaction)., Methods: RT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orléans, France). Capillary whole blood (CWB) samples from the fingertip taken at different time points after onset of the disease were tested with POC tests. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated., Results: Among 381 patients with symptoms of COVID-19 who went to the hospital for a diagnostic, 143 patients were RT-PCR negative. Results of test with POC tests were all negative for these patients, indicating a specificity of 100% for both POC tests. In the RT-PCR positive subgroup (n = 238), 133 patients were tested with COVID-PRESTO® and 129 patients were tested with COVID-DUO® (24 patients tested with both). The further the onset of symptoms was from the date of collection, the greater the sensitivity. The sensitivity of COVID-PRESTO® test ranged from 10.00% for patients having experienced their 1st symptoms from 0 to 5 days ago to 100% in patients where symptoms had occurred more than 15 days before the date of tests. For COVID-DUO® test, the sensitivity ranged from 35.71% [0-5 days] to 100% (> 15 days)., Conclusion: COVID-PRESTO® and DUO® POC tests turned out to be very specific (none false positive) and to be sensitive enough after 15 days from onset of symptom. These easy to use IgG/IgM combined test kits are the first ones allowing a screening with CWB sample, by typing from a finger prick. These rapid tests are particularly interesting for screening in low resource settings., Competing Interests: The point-of-care tests were provided free of charge by AAZ-LMB. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Background: Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species., Results: We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species., Conclusion: The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.

Calanus copepods are keystone species in marine ecosystems, mainly due to their high lipid content, which is a nutritious food source for e.g. juvenile fish. Accumulated lipids are catabolized to meet energy requirements during dormancy (diapause), which occurs during the last copepodite stage (C5). The current knowledge of lipid degradation pathways during diapause termination is limited. We characterized changes in lipid fullness and generated transcriptional profiles in C5s during termination of diapause and progression towards adulthood. Lipid fullness of C5s declined linearly during developmental progression, but more β-oxidation genes were upregulated in early C5s compared to late C5s and adults. We identified four possible master regulators of energy metabolism, which all were generally upregulated in early C5s, compared to late C5s and adults. We discovered that one of two enzymes in the carnitine shuttle is absent from the calanoid copepod lineage. Based on the geographical location of the sampling site, the field-samples were initially presumed to consist of C. finmarchicus. However, the identification of C. glacialis in some samples underlines the need for performing molecular analyses to reliably identify Calanus species. Our findings contributes to a better understanding of molecular events occurring during diapause and diapause termination in calanoid copepods.

Multiple substances (alcohol, tobacco, cannabis and other illicit drugs (OID)) have been frequently used in early adolescents maybe due to school, violence and mental-health difficulties. We investigated the associations between substance-use patterns and related difficulties among 1559 middle-school adolescents from north-eastern France (mean age 13.5 ± 1.3). They completed a questionnaire including socioeconomic features, school, violence and mental-health difficulties (school grade repetition, sustained physical/verbal violence, sexual abuse, perpetrated violence, poor social support, depressive symptoms and suicide attempt; cumulated number noted SVMD score ) and the time of their first occurrence during the life course. Data were analyzed using logistic and negative binomial regression models. Alcohol, tobacco, cannabis and OID use affected 35.2, 11.2, 5.6 and 2.8% of the subjects respectively. The risk of using tobacco only, alcohol and tobacco, alcohol plus tobacco and cannabis, or all alcohol, tobacco, cannabis and OID strongly increased with the SVMD score (socioeconomic features-adjusted odds ratio reaching 85). The risk began in early years in middle schools and then steadily increased, more markedly for elevated SVMD score . Exposure to several SVMDs may be a transmission vector towards the substance use, starting mostly with alcohol/tobacco, and then shifting to cannabis/OID. These findings help to understand substance-use risk patterns and identify at-risk adolescents., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Calanus finmarchicus and Calanus glacialis are keystone zooplankton species in North Atlantic and Arctic marine ecosystems because they form a link in the trophic transfer of nutritious lipids from phytoplankton to predators on higher trophic levels. These calanoid copepods spend several months of the year in deep waters in a dormant state called diapause, after which they emerge in surface waters to feed and reproduce during the spring phytoplankton bloom. Disruption of diapause timing could have dramatic consequences for marine ecosystems. In the present study, Calanus C5 copepodites were collected in a Norwegian fjord during diapause and were subsequently experimentally exposed to the water-soluble fraction of a naphthenic North Sea crude oil during diapause termination. The copepods were sampled repeatedly while progressing toward adulthood and were analyzed for utilization of lipid stores and for differential expression of genes involved in lipid metabolism. Our results indicate that water-soluble fraction exposure led to a temporary pause in lipid catabolism, suggested by (i) slower utilization of lipid stores in water-soluble fraction-exposed C5 copepodites and (ii) more genes in the β -oxidation pathway being downregulated in water-soluble fraction-exposed C5 copepodites than in the control C5 copepodites. Because lipid content and/or composition may be an important trigger for termination of diapause, our results imply that the timing of diapause termination and subsequent migration to the surface may be delayed if copepods are exposed to oil pollution during diapause or diapause termination. This delay could have detrimental effects on ecosystem dynamics.

Background: Carbapenemase-producing Enterobacteriaceae (CPE) have become a major public health issue. The objective of the present study was to prospectively assess the analytical performance of a CPE detection algorithm based on phenotypic tests (the screening test) and MALDI-ToF hydrolysis (the confirmatory test)., Methods: Over a 6-month period and based on a disk diffusion method, 74 carbapenem-resistant strains were included in this study., Results: Of the collected isolates, 54 turned out to be negative after phenotypic tests. Hence, 20 strains (including all of the CPEs) were checked with the confirmation test. Seven strains were positive. After molecular biology assessments in a reference center, three of the seven were found to be false positives. The algorithm had a negative predictive value and a sensitivity of 100%, a specificity of 77%, and a positive predictive value of 20%., Conclusion: The algorithm has a 24-hour turnaround time and helps to avoid using expensive molecular biology tests; we consider that it can be used on a routine basis for screening clinical strains., (© 2018 Wiley Periodicals, Inc.)

Advances in next-generation sequencing technologies and the development of genome-reduced representation protocols have opened the way to genome-wide population studies in non-model species. However, species with large genomes remain challenging, hampering the development of genomic resources for a number of taxa including marine arthropods. Here, we developed a genome-reduced representation method for the ecologically important marine copepod Calanus finmarchicus (haploid genome size of 6.34 Gbp). We optimized a capture enrichment-based protocol based on 2656 single-copy genes, yielding a total of 154 087 high-quality SNPs in C. finmarchicus including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric C. glacialis . Preliminary analyses of these markers revealed similar levels of genetic diversity between the two Calanus species, while populations of C. glacialis showed stronger genetic structure compared to C. finmarchicus . Using this powerful set of markers, we did not detect any evidence of hybridization between C. finmarchicus and C. glacialis . Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes., Competing Interests: The authors declare no competing interests.

Zooplankton provide the key link between primary production and higher levels of the marine food web and they play an important role in mediating carbon sequestration in the ocean. All commercially harvested fish species depend on zooplankton populations. However, spatio-temporal distributions of zooplankton are notoriously difficult to quantify from ships. We know that zooplankton can form large aggregations that visibly change the color of the sea, but the scale and mechanisms producing these features are poorly known. Here we show that large surface patches (>1000 km 2 ) of the red colored copepod Calanus finmarchicus can be identified from satellite observations of ocean color. Such observations provide the most comprehensive view of the distribution of a zooplankton species to date, and alter our understanding of the behavior of this key zooplankton species. Moreover, our findings suggest that high concentrations of astaxanthin-rich zooplankton can degrade the performance of standard blue-green reflectance ratio algorithms in operational use for retrieving chlorophyll concentrations from ocean color remote sensing.

Planktonic copepods of the genus Calanus play a central role in North Atlantic/Arctic marine food webs. Here, using molecular markers, we redrew the distributional ranges of Calanus species inhabiting the North Atlantic and Arctic Oceans and revealed much wider and more broadly overlapping distributions than previously described. The Arctic shelf species, C. glacialis , dominated the zooplankton assemblage of many Norwegian fjords, where only C. finmarchicus has been reported previously. In these fjords, high occurrences of the Arctic species C. hyperboreus were also found. Molecular markers revealed that the most common method of species identification, prosome length, cannot reliably discriminate the species in Norwegian fjords. Differences in degree of genetic differentiation among fjord populations of the two species suggested that C. glacialis is a more permanent resident of the fjords than C. finmarchicus We found no evidence of hybridization between the species. Our results indicate a critical need for the wider use of molecular markers to reliably identify and discriminate these morphologically similar copepod species, which serve as important indicators of climate responses., (© 2017 The Authors.)

Calanus glacialis , a marine planktonic copepod, is a keystone species in the Arctic Ocean. In this study, we shotgun sequenced the total DNA of one C. glacialis individual, using the NextSeq ® Illumina platform, in order to determine its mitochondrial genome sequence. We successfully assembled and annotated this 20,674 bp long sequence, which included 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. Common gene-coding regions of 19 other species were used to reconstruct a phylogenetic tree, using mitogenomes of the phylogenetically closest copepods available. The new resource described here constitutes a tool of interest for better understanding the structure and dynamics of C. glacialis populations., Competing Interests: The authors have no conflict of interest to declare., (© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Clival osteomyelitis is a potentially life-threatening infection that can occur in healthy children. It can be related to congenital anomalies. We report the case of a 7-year-old boy with Streptococcus intermedius and Fusobacterium clival osteomyelitis arising from a Thornwaldt cyst situated in a fossa navicularis magna of the occipital bone. Multidisciplinary management is necessary to ensure rapid improvement and complete healing., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Background: Aggregatibacter aphrophilus, a commensal of the oro-pharyngeal flora and member of the HACEK group of organisms, is an uncommonly encountered clinical pathogen. It has already been described as the causative agent of brain abscesses, empyema, meningitis, sinusitis, otitis media, bacteriemia, pneumonia, osteomyelitis, peritonitis, endocarditis and wound infections. Herein we report the first case of bartholinitis due to A. aphrophilus., Case Presentation: A 33-year-old woman was admitted for a 3-day genital pain without fever and urinary functional signs. The abscess was incised and drained; A. aphrophilus was the only micro-organism that grew from the pus. The patient received no antibiotics; the clinical course was favourable., Conclusion: This case highlights the importance of an effective treatment of recurrent bartholinitis such as a cold resection of the gland. It is presented for its rarity.